Detecting Human Caused Population Collapse in Orang-utans from Genetic Data

I’m gonna be sharing with you another state-of-the-orang-utan-union type article, however this time it is in the form of a scientific paper. The paper was just published in PLoS Biology, an open access academic journal… so you can read the first hand scientific accounts from anywhere. It is titled, “Genetic Signature of Anthropogenic Population Collapse in Orang-utans” and here’s the abstract (I’ve bolded what I think is the most impacting part of this paper),

“Great ape populations are undergoing a dramatic decline, which is predicted to result in their extinction in the wild from entire regions in the near future. Recent findings have particularly focused on African apes, and have implicated multiple factors contributing to this decline, such as deforestation, hunting, and disease. Less well-publicised, but equally dramatic, has been the decline in orang-utans, whose distribution is limited to parts of Sumatra and Borneo. Using the largest-ever genetic sample from wild orang-utan populations, we show strong evidence for a recent demographic collapse in North Eastern Borneo and demonstrate that this signature is independent of the mutation and demographic models used. This is the first demonstration that genetic data can detect and quantify the effect of recent, human-induced deforestation and habitat fragmentation on an endangered species. Because current demographic collapses are usually confounded by ancient events, this suggests a much more dramatic decline than demographic data alone and emphasises the need for major conservation efforts.”

The basic premise of the publication is that defrestation has impacted populations of wild orang-utans in North Eastern Borneo to such determental levels that the gene pool can’t support a viable population even if things turn for the better. That was a bit hard for the authors to prove because the effects of very recent human caused population fragmentation among orang-utans on genetic diversity are typically difficult to demonstrate. How can one attribute human caused population fragmentation as the sole factor? What if other things are going on?

In order to answer that question and factor out any other variables the authors first limited their study to orang-utan populations in the,

“Lower Kinabatangan floodplain in Eastern Sabah, a region that has experienced large-scale commercial timber exploitation and agriculture since the mid-1950s. Faecal and hair samples were collected from wild orang-utans during boat surveys along the Kinabatangan River or during line transects to estimate nest densities. Two hundred different animals were genetically identified using 14 microsatellites.”

So they have a pretty large sample size from a region where there’s been a long standing history of human impacted ecological change. That makes for a pretty strong foundation upon to make conclusions. Next, they basically ran three different but complementary tests in order to detect, quantify, and date the decline in orang-utan populations. Here’s a two part summary of the three tests:

  1. “The first approach is based on summaries of the allelic frequency spectrum and was used to detect either a population expansion or decline. It relies on the loss or excess of rare alleles expected in bottlenecked or expanding populations, respectively, and uses simulations under different mutation models to detect departures from mutation-drift equilibrium.”
  2. “The two other approaches used were Bayesian methods using the information from the full allelic distributions and shall be referred to as the Beaumont and the Storz and Beaumont method… The two Bayesian methods were applied to two subsets of the data for computational reasons.”

From these tests the authors concluded the following results. The first test yielded an observation that, “all nine samples exhibit a strong and significant signal for a population bottleneck, through the loss of rare alleles.” That just means orang-utans are losing their diversity. There’s no definitive conclusion on what that will do, and when that will cause the orang-utan population to collapse… but it is pretty indicative that once you lose diversity, the probability of survival amongst your population reduces. The second test confirmed the conclusion from the first test or in their words, “the present-day genetic structure of orang-utans is strongly influenced by a dramatic decrease in population size, with no support for growing or even stable populations.” And the last test quanitified a date upon which the population of orang-utans will collapse due to a lack of genetic diversity… and that will be on or before 210 years from now.

That’s such a low blow. I don’t know which is worse news, that orang-utan habitats will be erased within 15 years if we continue deforestation at the rates they are going on at or that this is all futile and orang-utans are so endangered that there’s no hope for them a couple centuries down the line. Now there’s a possibility that the computer models, algorithms, and statistical analysis the authors of this paper used are just probabilities… but it does seem that either way orangs-utans are screwed.

In the last century or so, we have killed off 95% of orang-utans. That statistic by itself is crazy. They are a unique and vital species of great ape. They are the only other great ape, other than humans, who live outside of Africa, and deserve our best efforts for conservation. The first thing we must do, as I advocated earlier, is to cut our dependance on illegal logging. That is something we can all do personally. Use less fresh paper, recyle and reuse. The next thing that needs to be done is to step up efforts in creating a diverse genetic population of orang-utans in captivity. That’s all we got. I hope zoological insitutions step up to the plate and devise a plan to accomplish this common goal…

2 thoughts on “Detecting Human Caused Population Collapse in Orang-utans from Genetic Data

  1. Yes, we must somehow preserve their habitat, or captive breeding programs will only maintain a captive population — tragic for a wide-ranging, mostly-solitary ape.

    On a personal level, to does help to “reduce, reuse, and recycle,” though we may be half a world away — we’re all connected. Our reproductive choices are by far the most significant way we can help. By choosing to not create another of ourselves, we eliminate one lifetime of consumption. To find out how much wildlife habitat we preserve by not creating another human, go here and click on “Download national footprint results.”

    In North America, we avoid the loss of 24 acres of biologically productive land for about 75 years.

    There are more humans born each day than the populations of great apes combined.

    Les Knight

  2. Hey Les, thanks for the input. Your suggestion is very helpful too.

    At a minimum people can decide not to have children or just have one, and create a dramatic change. Since there will be less demand for food and other resources needed to raise the kids, then there wouldn’t necessarily be as much logging, pollution, etc.

    I appreciate the comment, Kambiz.

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